GO enrichment for RNA-Seq

PFS

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Join Date: Mar 2010

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GO enrichment for RNA-Seq

02-28-2011, 09:05 AM

I am looking for a way to display GO-enrichment of RNA-Seq (e.g. pie charts/graphs for the most enriched GO categories).

I have used the R package GoSeq to identify the significantly enriched GO terms, but I would like to get more information than just a list of GOIDs.

I was thinking of retrieving the genes associated with the enriched GOIDs and then use GoFinder to perform the enrichment analysis and plot the graph.

How do I get the genes associated with the GOIDs from GoSeq?

Thanks,
PFS

ps: I understand GoFinder will not take care of the length-bias due to RNA-Seq, but I figured that if I first perform the analysis with goseq, then grab only the genes associated with the GOIDs identified by goseq, and repeat the analysis with these genes only, I should be able to avoid the bias. Is that correct?
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